Celiac disease (CD) is common in both children and adults, and is characterized by abnormal small intestinal mucosa, permanent intolerance to gluten, and full recovery of clinical, biochemical, and histological findings when gluten is removed from the diet (although some patients are refractory). As a result, individuals diagnosed with CD are usually placed on a strict gluten-free diet. Small intestinal biopsy is mandatory for establishing the diagnosis of CD, but the diagnosis of CD is complicated by the fact that the disease may be silent, or may be present with atypical findings. Therefore, serological markers are used both to select patients requiring biopsy and to monitor response and adherence to a gluten-free diet.
Anti-endomysial antibodies have a sensitivity and specificity of close to 100% in the diagnosis of CD in individuals without immunoglobulin A (IgA) deficiency. Anti-tissue transglutaminase (tTG) antibodies are also highly sensitive and specific for diagnosing CD. In fact, a recent Celiac Advisory Board has recommended that assays for detecting only these two antibodies should be sufficient to diagnose CD. When serology and biopsy are inconclusive, testing for specific human leukocyte antigen (HLA) genes associated with CD may be helpful in screening for the disease. If particular polymorphisms in these genes are not present, it is unlikely that the individual will develop CD. A positive HLA test, however, does not mean that the individual has the disease, since these genes are also common in the general population.
Susceptibility to celiac disease is associated with specific human leukocyte antigen (HLA) DQ haplotypes HLA-DQ2 and HLA-DQ8 (Sollid et al., J. Exp. Med., 169:345-350 (1989); Sollid et al., Nat. Clin. Pract. Gastroenterol. Hepatol., 2(3):140-147 (2005); Koning, Gastroenterology, 129:1294-1301 (2005)). The presence of HLA-DQ2 or HLA-DQ8 is necessary for the development of CD, but not sufficient, since these haplotypes are present in up to 30% of healthy individuals and in a much higher percentage of persons at risk for CD (Sollid et al., J. Exp. Med., 169:345-350 (1989); Liu et al., Gastroenterology, 128(4 suppl 1):S33-S37 (2005); Margaritte-Jeannin et al., Tissue Antigens, 63:562-527 (2004)). Although other genes not yet identified likely play important roles in predisposing to the development of CD, confirmed CD patients carrying neither the DQ2 nor the DQ8 haplotype are extremely uncommon, and those not carrying at least half of the DQ2 haplotype are rare (Koning et al., Best Pract. Res. Clin. Gastroenterol., 19(3):373-387 (2005), Karell et al., Hum. Immunol., 64:469-477 (2003), Sollid et al., Clin. Gastroenterol. Hepatol., 3:843-851 (2005), Babron et al., Eur. J. Hum. Genet., 11:828-834 (2003)).
Unfortunately, genetic screening to ascertain susceptibility to CD has been of limited clinical utility because its scope has been restricted to excluding the diagnosis in individuals not carrying either the DQ2 or DQ8 haplotype (Hadithi et al., Ann. Intern. Med., 147(5):294-302 (2007); Liu et al., Gastroenterology, 128(4 suppl 1):S33-S37 (2005)). This approach is very helpful to the roughly 40% of persons at risk for CD, on the basis of family history or clinical symptoms, who are found to be negative for HLA-DQ2 and HLA-DQ8, but it provides little useful information for the person at risk who does carry one or both of these haplotypes. For the full potential of HLA-DQ genotyping as a CD screening tool for persons at risk to be realized, the focus of risk determination must shift, from the haplotypes themselves to the heterodimers formed by the α and β chains that are the gene products coded by these HLA-DQ alleles (Koning, Gastroenterology, 129:1294-1301 (2005); Bourgey et al., Gut, 56:1054-1059 (2007)) (see, FIG. 1) (adapted from Koning, 2005).
These DQ heterodimers are expressed on the cell surface of antigen-presenting cells in the lamina propria of the small intestine (Koning, Gastroenterology, 129:1294-1301 (2005); Koning et al., Best Pract. Res. Clin. Gastroenterol., 19(3):373-387 (2005); Sollid et al., Nat. Clin. Pract. Gastroenterol. Hepatol., 2(3):140-147 (2005); Sollid et al., Clin. Gastroenterol. Hepatol., 3:843-851 (2005)). The disease-associated DQ2 heterodimer, and to a much lesser extent the DQ8 heterodimer, avidly bind certain peptide fragments derived from gluten and present them to CD4 T cells (FIG. 2) (Sollid et al., Nat. Clin. Pract. Gastroenterol. Hepatol., 2(3):140-147 (2005); Sollid et al., Clin. Gastroenterol. Hepatol., 3:843-851 (2005); Kim et al., Proc. Natl. Acad. Sci. USA, 101:4175-4179 (2004); Qiao et al., J. Immunol., 173:1757-1762 (2004)). This, in turn, stimulates a proliferation of T cells and cytokines, which appears to be a necessary, but not sufficient, first step in the pathogenesis of CD (Koning, Gastroenterology 129:1294-1301 (2005); Koning et al., Best Pract. Res. Clin. Gastroenterol., 19(3):373-387 (2005)). Most importantly, the properties of DQ heterodimers formed from α and β chains coded by genes located in trans (i.e., from opposing chromosomes) are identical to those formed from α and β chains coded by genes located in cis (i.e., from the same chromosome) (Tollefsen et al., J. Clin. Invest., 116:2226-2236 (2006), Koning, Gastroenterology, 129:1294-1301 (2005); Vader et al., Proc. Natl. Acad. Sci. USA, 100:12390-12395 (2003)). Thus, knowing the type and proportion of heterodimers that correspond to each genotype has the greatest potential of determining the genetic risk for CD.
Studies of CD epidemiology including both genetic and serologic data done in the U.S. (Fasano, Gut, 52:168-169 (2003)), as well as the majority of European studies (Dolinsek et al., Wien Klin Wochenschr., 116 Suppl 2:8-12 (2004); Karell et al., Hum. Immunol., 64:469-477 (2003); Karinen et al., Scand. J. Gastroenterol., 41:1299-1304 (2006); Babron et al., Eur. J. Hum. Genet., 11:828-834 (2003); Dube et al., Gastroenterology, 128(4 suppl 1):S57-S67 (2005)), have been limited to reporting the presence or absence of DQ2- or DQ8-associated haplotypes or their constituent alleles.
In view of the foregoing, what is needed in the art are methods for predicting whether an individual is at risk of developing celiac disease (CD), as well as methods that stratify the risk for celiac disease. The present invention satisfies these as well as other needs.